Microbiome in IgG4 & systemic sclerosis, US, case-control
313 fecal samples from adults and elderly people in the USA, comparing IgG4 patients and intestinal systemic sclerosis patients with healthy controls; case-control design. machine-written summary
313 samples · 313 runs · US · Adult · 2021 · 2.01 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,836 sample values (age, collection date, country, health condition, health condition detail, medication, medication detail, sex) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 313 sample values (subject id) · PMC12659350, PMC7919092, PMC8429070 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 282 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 313 | 100% | ||||
| country | 313 | 100% | 313 | |||
| health_condition | 313 | 100% | 313 | |||
| subject_id | 313 | 100% | 313 | |||
| age_at_collection_days | 313 | 100% | 313 | |||
| health_condition_detail | 313 | 100% | 313 | |||
| sex | 313 | 100% | 313 | |||
| collection_date | 148 | 47% | 148 | |||
| medication | 75 | 24% | 75 | |||
| medication_detail | 48 | 15% | 48 |
- Congruent microbiome signatures in fibrosis-prone autoimmune diseases: IgG4-related disease and systemic sclerosis. 2021 PMID 33648559 PMC7919092 own_data
- Cytokine-specific autoantibodies shape the gut microbiome in autoimmune polyendocrine syndrome type 1. 2021 PMID 33819509 PMC8429070 own_data
- Protein language models uncover carbohydrate-active enzyme function in metagenomics. 2025 PMID 41299229 PMC12659350 unsure
Archive description
Microbiome characterization of IgG4 patients and Intestinal Systemic Sclerosis patients
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult and elderly by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- body site study.title · “Gut Microbiome characterization of”
- body site study.description · “IgG4 patients and Intestinal Systemic Sclerosis patients”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- life stage sample.attr.age · “66 (n=95/313)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN17765046 | age_at_collection_days | 31018.0 | R1 | 0.85 | sample.attr.age | 85 |
| SAMN17765046 | collection_date | 2015-01/2017-12 | R1 | 0.90 | biosample.attribute:collection_date | 2015-01/2017-12 |
| SAMN17765046 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA |
| SAMN17765046 | health_condition | autoimmune_inflammatory | R1 | 0.50 | biosample_attr | IgG4RD |
| SAMN17765046 | health_condition_detail | activedisease: yes | R1 | 0.85 | sample.attr.activedisease | 1 |
| SAMN17765194 | health_condition_detail | Controls | R1 | 0.85 | biosample.attribute:cohort | cohort: Controls |
| SAMN17765047 | medication | corticosteroid;immunosuppressant_or_biologic | R1 | 0.85 | biosample.attribute:prednisone;rtx | prednisone: 1 | rtx: 1 |
| SAMN17765048 | medication | immunosuppressant_or_biologic | R1 | 0.85 | biosample.attribute:rtx | rtx: 1 |
| SAMN17765053 | medication | immunosuppressant_or_biologic | R1 | 0.90 | biosample.attribute:other_drugs | cyclophosphamide |
| SAMN17765054 | medication | corticosteroid | R1 | 0.85 | biosample.attribute:prednisone | prednisone: 1 |
| SAMN17765053 | medication_detail | cyclophosphamide | R1 | 0.90 | biosample.attribute:other_drugs | cyclophosphamide |
| SAMN17765046 | sex | female | R1 | 0.90 | sample.attr.sex | female |
| SAMN17765046 | subject_id | SAMN17765046 | R3 | 0.75 | design.one_sample_per_subject:fulltext | we sought to characterize the stool microbiome sampled at a single time point of patients diagnosed with IgG4-RD (N = 58) and SSc (N = |
Sequencing
313 runs over 313 samples · mean 2.44 Gbp per run (median 2.01 Gbp, total 763.15 Gbp; 313 runs with a base count) · layout PAIRED 313 · platform ILLUMINA 313 · models Illumina HiSeq 2500 (313) · 90% of runs with a Sandpiper profile · first public 2021-02-04
Authors (45)
Plichta DR first · Somani J · Pichaud M · Wallace ZS · Fernandes AD · Perugino CA · Lähdesmäki H · Stone JH · Vlamakis H · Chung DC · Khanna D · Pillai S · Xavier RJ last · Petersen A first · Jokinen M · Liebisch G · Gronwald W · Dettmer K · Oefner PJ · Ranki A · Argentini C first · Lugli GA · Tarracchini C · Fontana F · Mancabelli L · Viappiani A · Anzalone R · Angelini L · Alessandri G · Longhi G · Bianchi MG · Taurino G · Bussolati O · Milani C · van Sinderen D · Turroni F · Ventura M last · Thurimella K first · Mohamed AMT · Li C · Vatanen T · Graham DB · Owens RM · La Rosa SL · Bacallado S
Downloads
PRJNA615162.csv.gz (10.2 KB) · parquet (85.1 KB) — all 313 samples, every field with route and confidence · PRJNA615162_determinations.csv.gz (15.3 KB) — 2,149 evidence rows